Question: Error when runing dotplot with enrichGO results
2
gravatar for dingailuma
17 months ago by
dingailuma20
dingailuma20 wrote:

I used to run the exactly same commands in Rstudio and no errors occured.

ego <- enrichGO(gene=gene_EntrezID,OrgDb = org.Hs.eg.db,keytype = "ENTREZID", ont="BP",readable = T,pvalueCutoff = 0.001,qvalueCutoff = 0.001)
dotplot(ego,colorBy = "pvalue",showCategory = 10)

But now this error jumps out:

Error in unique.default(x, nmax = nmax) : 
  unique() applies only to vectors

I can't find out the reason, could someone help me please ? Thx !

dotplot clusterprofier • 882 views
ADD COMMENTlink modified 10 months ago by Anthony10 • written 17 months ago by dingailuma20

Another question, anyone know how to set compareCluster results readable ? (I mean transfer ENTREZID to GENE SYMBOL) ? Thx again !

ADD REPLYlink written 17 months ago by dingailuma20
ego@result
ADD REPLYlink written 11 months ago by Walid0

Hi,

I never used this package, but looking at your error only, it seems to indicate that your "ego" object is not a vector. Can you see what "ego" is?

head(ego)

or

str(ego)
ADD REPLYlink written 17 months ago by b.nota4.0k

I found if I use plot() instead of dotplot() , then no errors . Wierd ! Maybe some bugs when authors updating the clusterprofiler package.

ADD REPLYlink written 17 months ago by dingailuma20

or class(ego). My money is on an unexpected factor.

ADD REPLYlink written 17 months ago by WouterDeCoster29k
1
gravatar for Anthony
10 months ago by
Anthony10
Anthony10 wrote:

To avoid the error, use DOSE::dotplot instead of dotplot.

The error occurs when you use the lattice package, which may have been loaded by another package you were using:

The following object is masked from ‘package:clusterProfiler’:

    dotplot
ADD COMMENTlink modified 10 months ago • written 10 months ago by Anthony10
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